Thesis

The effect of phosphorothioate-modified DNA and nanoparticle size on quantitative enhanced Raman scattering

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Awarding institution
  • University of Strathclyde
Date of award
  • 2013
Thesis identifier
  • T13678
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Abstract
  • Surface-enhanced Raman scattering (SERS) has been used successfully as an ultrasensitive technique for the direct analysis of dye-labelled oligonucleotides using aggregated silver nanoparticles. Key to this technique are the SERS probe and SERS substrate. Initial studies were made on the detection of phosphorothioate modified TAMRA-labelled oligonucleotides whereby a non-bridging oxygen atom in the phosphodiester backbone is replaced by sulfur. TAMRA-labelled phosphorothioate oligonucleotides with the same base pair sequence but different number of modified phosphate unites were compared to unmodified TAMRA-labelled oligonucleotides using silver nanoparticles (AgNP) as SERS substrates using different aggregation agents. Furthermore the investigation was extended to study the effect of modification in the detection of double stranded DNA (dsDNA). The focus was then turned to the SERS substrate since spherical and monodispersed silver nanoparticles are ideal for fundamental research as the contribution from size and shape can be accounted for in the experimental design. Different methods to produce size tuneable AgNP's were investigated to study in detail the effect of modified and unmodified dye-labelled oligonucleotides, thiophenol (TP), rhodamine 6G (R6G) and malachite green oxalate (MGO) on the SERS response. The results obtained reflect the importance of each component of SERS. The phosphorothioate modifications, although their affinity towards silver surfaces can improve the DNA limit of detection (LOD), it also depends on the position and number of modifications and on the aggregating agent used which in itself also effects the LOD of DNA. The same applies for the SERS substrate where an increase in particle size results in an increased enhancement of the analyte's Raman signal but further size increments leads to a decrease in SERS intensity due to other factors such as scattering. This demonstrates the importance of choosing the right experimental setups for DNA SERS analysis, as to obtain the right balance where all factors work synergistically with each other.
Resource Type
DOI
Date Created
  • 2013
Former identifier
  • 1027060

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